Figure 8
From: Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters
HMM simulations demonstrate increased signal strength as a result of PyPu depletion. Sequence logos resulting from sequence generation using an HMM incorporating rules for describing PyPu usage (see Materials and methods). Specifically, PyPu dinucleotides are not allowed in positions where they would introduce new initiation sites with more favorable TATA-TSS distances (-31, -32, and so on until the known spacing occurs). This results in an increase of Py nucleotides upstream of the TSS. bp, base pairs; HMM, Hidden Markov Model; Pu, purine; Py, pyrimidine; TSS, transcription start site.